Contacts of the strand formed by residues 571 - 576 (chain B) in PDB entry 5N4D
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 571 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B ALA* 3.6 5.2 - - + +
493B GLN* 3.9 27.8 - - + +
557B ALA* 3.9 20.2 - - + +
560B LEU* 4.3 10.8 - - + -
561B VAL* 3.7 28.5 - - + -
566B ALA* 4.1 14.1 - - + -
569B GLY* 3.6 1.8 - - - -
570B LYS* 1.3 77.9 - - - +
572B ALA* 1.3 70.5 + - - +
594B THR 4.2 11.8 + - - +
595B PHE* 3.4 12.4 - - + +
596B GLY* 2.9 25.2 + - - +
597B ALA 4.6 0.2 - - - -
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Residues in contact with ALA 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B ALA 2.8 13.4 + - - +
492B ILE* 4.4 5.6 - - + -
493B GLN* 2.7 34.9 + - - +
570B LYS 3.8 1.2 + - - -
571B VAL* 1.3 74.4 - - - +
573B ILE* 1.4 57.0 + - - +
597B ALA* 3.2 22.7 - - + +
718B ILE* 3.6 37.0 - - + -
722B LEU* 4.1 4.3 - - + -
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Residues in contact with ILE 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493B GLN* 3.2 20.0 - - + +
553B PHE* 3.6 21.3 - - + -
571B VAL* 4.5 0.7 - - + -
572B ALA* 1.4 79.7 - - - +
574B ASN* 1.3 65.0 + - - +
583B VAL* 3.9 22.4 - - + +
586B SER* 4.0 7.2 - - - -
587B ILE* 3.8 24.9 - - + -
595B PHE* 3.5 42.4 - - + -
597B ALA 3.0 13.1 + - - +
598B ALA* 3.4 7.8 - - + -
599B VAL* 2.9 26.3 + - - +
718B ILE* 5.2 0.7 - - - +
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Residues in contact with ASN 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B ILE* 4.9 4.3 - - + -
493B GLN 3.0 6.8 + - - +
494B TYR* 3.3 31.1 - - + -
495B GLY 3.2 23.2 + - - +
553B PHE* 4.6 0.9 - - - -
573B ILE* 1.3 77.9 - - - +
575B GLY* 1.3 61.4 + - - +
583B VAL* 3.7 8.4 - - - +
599B VAL* 2.8 36.7 + - + +
601B GLU* 2.8 26.3 + - - +
714B LYS* 3.5 20.4 + - - +
715B TRP* 3.8 20.6 - - + -
718B ILE* 5.1 1.6 - - + -
13D HIS* 3.9 0.2 - - - -
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Residues in contact with GLY 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B TYR* 4.0 10.8 - - - -
495B GLY 3.5 15.5 - - - -
574B ASN* 1.3 81.2 - - - +
576B ALA* 1.4 61.3 + - - -
579B GLY 3.5 14.8 - - - -
580B GLY* 3.6 4.3 + - - -
583B VAL* 3.7 2.6 - - - +
599B VAL 3.5 3.2 + - - +
600B PRO* 3.8 0.2 - - - +
601B GLU* 2.9 26.8 + - - +
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Residues in contact with ALA 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B TYR* 4.6 6.3 + - - +
495B GLY 4.5 0.8 + - - -
496B TYR* 3.6 11.5 - - - -
575B GLY* 1.4 73.2 - - - +
577B SER* 1.3 67.5 + - - +
578B ASN 3.2 0.5 + - - -
579B GLY* 2.8 20.7 + - - -
580B GLY 3.5 2.7 - - - +
601B GLU* 3.2 27.1 - - + +
12D GLU* 5.3 10.3 - - + +
13D HIS* 4.3 13.0 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il